tbuckley/cabot-search huggingface dataset:
Abstract 5006: Discovery of novel heterobifunctional degraders of mutant EGFR proteins for NSCLCs harboring various EGFR mutations
Authors: Dong Hyuk Ki, Min Sung Joo, Joonwoo Nam, Hunmi Choi, Kyoungwan Seo, Eun-Jung Kim, Jiyeon Kim, Chulwon Kim, Jimmy Taiguang Jin, Wooseok Han
Journal: Cancer Research (2023)

Abstract Abnormal expression and activation of Epidermal Growth Factor Receptor (EGFR) contribute to malignancy development, especially in non-small cell lung cancers (NSCLCs). Although the first- to third-generation EGFR small molecule inhibitors have made significant progress in the treatment of EGFR mutant NSCLC patients, acquired mutations have been developed rapidly, resulting in drug resistance. Targeted protein degradation (TPD) technologies including PROteolysis Targeting Chimeras (PROTACs) have recently emerged as a promising alternative modality to address the confronting issues of small molecule inhibitors such as drug resistance. Recently, we have developed a series of heterobifunctional degraders of EGFR mutant proteins, which showed strong degradation ability against a variety of mutant EGFRs including triple mutants with C797S. DC50 (half-maximal degradation concentrations) values of the degraders were obtained using HiBiT assay in NCI-H1975 (EGFR L858R/T790M), HCC827 (EGFR Del19), and H1299 (EGFR WT) cells. Our lead compounds demonstrated excellent EGFR degradation potency with high selectivity against EGFR wild type. Moreover, C-09045, C-09066, and C-13951 strongly inhibited the cell growth of Ba/F3 cells harboring one of the EGFR mutations including L858R/C797S, Del19/C797S, L858R/T790M/C797S, Del19/T790M/C797S, and Exon20 NPH insertion. By contrast, these compounds showed much weaker potency in normal lung fibroblast (HFL-1) and Ba/F3 cells harboring EGFR wild-type. In PK analysis, C-09066 showed good oral bioavailability in mice (F%=41.4) with desirable pharmacokinetic parameters and robust tumor growth inhibition efficacy in the NCI-H1975 EGFR L858R/T790M/C797S xenograft and the Ba/F3 Del19/C797S allograft mouse models. In summary, we have identified selective, potent, and orally bioavailable degraders of various EGFR mutant proteins with broad spectrum anti-tumor efficacy both in vitro and in vivo. Citation Format: Dong Hyuk Ki, Min Sung Joo, Joonwoo Nam, Hunmi Choi, Kyoungwan Seo, Eun-Jung Kim, Jiyeon Kim, Chulwon Kim, Jimmy Taiguang Jin, Wooseok Han. Discovery of novel heterobifunctional degraders of mutant EGFR proteins for NSCLCs harboring various EGFR mutations. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5006.
Abstract 2587: AHR-WLS complex correlates with poor prognosis in B-cell precursor acute lymphoblastic leukemia
Authors: Li-Ting Wang, Shih-Hsien Hsu
Journal: Cancer Research (2023)

Abstract B cell precursor acute lymphoblastic leukemia (BCP ALL), the most common childhood cancer, is a malignant disorder that originates from the lymphoid precursor cells committed to B-cell lineage in the bone marrow. Although genetic abnormalities disturb the normal maturation process of these lymphoid precursor cells resulting in the formation of leukemia cells and suppression of normal hematopoiesis, environmental factors seem to modulate disease progression. The underline mechanism is not clear yet. In this study, we hypothesize environmental pollutants-AHR and small molecule chaperone-WLS are involved in promoting the oncogenic effect and disease relapse of BCP-ALL leukemia cells and inhibiting normal hematopoietic function. Here, we show that Indeno [1,2,3-cd] pyrene (IP) promotes oncogenic activities in vitro and in vivo. Mechanistically, IP treatment activates AHR-IDOs axis to enhance tryptophan metabolism and bioactive metabolite- kynurenine (kyn) level, further promoting kyn-AHR signal enhanced loop. In orthotopic xenograft mouse model, IP treatment decreases disease relapse time and increases cell population of BCP ALL. These results show PAH (IP) exposure promotes the disease progression of BCP ALL. Citation Format: Li-Ting Wang, Shih-Hsien Hsu. AHR-WLS complex correlates with poor prognosis in B-cell precursor acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2587.
Abstract 5754: Determining the regulatory logic of breast cancer cells using single-cell multi-omics
Authors: Matthew J. Regner, Aatish Thennavan, Susana Garcia-Recio, Kamila Wisniewska, Philip M. Spanheimer, Joel S. Parker, Charles M. Perou, Hector L. Franco
Journal: Cancer Research (2023)

Abstract Cancer cells rewire regulatory elements scattered throughout the genome (such as enhancers) to drive aberrant gene expression. Thus, deconvoluting the regulatory mechanisms that contribute to oncogenic gene expression in cancer cells is key to understanding tumor biology. To this end, we have charted the transcriptional and epigenetic landscape of breast cancer at single-cell resolution to quantitatively link variation in chromatin accessibility to gene expression across malignant and non-malignant cell types. Our comprehensive dataset profiles the chromatin landscape (scATAC-seq) in concert with the transcriptional profiles (scRNA-seq) of 4 breast cancer cell lines, 12 primary breast tumors, and 4 normal mammary reduction tissue specimens collected and processed immediately after surgical resection. This dataset, encompassing over 250,000 individual cells, allowed us to define the regulatory logic of cancer cells by 1) revealing how the epigenome underlies cellular heterogeneity of these tumors in comparison to normal mammary tissue, 2) defining how malignant cells hijack enhancer elements to drive key transcriptional programs in a subtype-specific manner, and 3) annotating which cancer-specific enhancer-to-gene connections portend a worse outcome in patients. Notably, we discovered that cancer cells acquire de novo non-coding enhancer elements to modulate hallmark cancer pathways that were previously hidden using bulk genomics approaches. This highlights the potential for cancer-specific enhancers to serve as markers with diagnostic and prognostic potential, or even serve as tractable targets for therapeutic intervention. Together these data enable the annotation of the cellular composition, transcriptional, and epigenetic landscape of breast tumors to help pinpoint clinically relevant mechanisms of tumorigenesis. Citation Format: Matthew J. Regner, Aatish Thennavan, Susana Garcia-Recio, Kamila Wisniewska, Philip M. Spanheimer, Joel S. Parker, Charles M. Perou, Hector L. Franco. Determining the regulatory logic of breast cancer cells using single-cell multi-omics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5754.
Abstract 1728: Exosomal delivery of Fas-associated factor 1 (FAF1), a multifunctional tumor suppressor and genuine exosome cargo, effectively antagonizes tumor growth
Authors: Jeong-Hoon Han, DaeHo Park, Bumjun Jung, Hyeong-Gwon Yoo, Kyung-Ok Cho, Eunhee Kim
Journal: Cancer Research (2023)

Abstract Introduction: Exosomes are extracellular vesicles of 30-150 nm and can stably deliver their cargos to the target with low immunogenicity and efficient transmission. FAF1 is a genuine exosome cargo and, therefore, loaded into exosomes without additional engineering. FAF1 is a tumor suppressive protein with multifunctional roles including death-promotion (both apoptosis and necrosis), cell cycle arrest, anti-inflammation, and anti-angiogenesis. FAF1 also inhibits metastasis via inhibition of TGF-β pathway. Moreover, FAF1 elicits low expression profiles in several types of cancer. Therefore, this study examined whether exosomal delivery of FAF1 is a plausible strategy for anti-tumor therapeutics. Methods: Stable suspension cells originated from HEK293 cells inducibly overexpressing FAF1 were screened using Tet on-off system to avoid cell death due to continuous FAF1 expression. FAF1 was overexpressed by Doxycycline induction and the amounts of FAF1 loaded on exosomes were normalized by exosome markers. The efficacy of exosomal FAF1 was evaluated in mouse xenograft models implanted with various human carcinoma cells. Results: Cell lines showing FAF1 expression with more than 3 fold of control cells were picked. Among FAF1-overexpressing cells, F5-3 cell line showing highest expression of exosomal FAF1 (showing 23 fold of FAF1 loading efficiency compared to parental cells) was used for exosomal source for in vivo experiments. Furthermore, F5-3 produced about 70 times of exosomal FAF1 when compared to that of HEK293 cell in the same volume of culture medium. The exosomal FAF1 produced in F5-3 cells inhibited tumor growth in various cancer types including lung, breast, liver, and pancreas in mouse xenograft models. In addition, exosomal FAF1 consistently demonstrated superior tumor-suppressive potential to soluble FAF1 in all tumors investigated in this study. Also, there were no serious side effects based on weight changes. Conclusion: This study demonstrated the tumor-suppressive potential of exosomal FAF1, demonstrating the feasibility of exosomal delivery of FAF1 as an efficient therapeutic measure. Furthermore, the selective and massive production properties of F5-3 cell realizes efficient and scalable production of exosomal FAF1. Citation Format: Jeong-Hoon Han, DaeHo Park, Bumjun Jung, Hyeong-Gwon Yoo, Kyung-Ok Cho, Eunhee Kim. Exosomal delivery of Fas-associated factor 1 (FAF1), a multifunctional tumor suppressor and genuine exosome cargo, effectively antagonizes tumor growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1728.
Abstract 3120: Sex differences in pediatric cancer genomics
Authors: Jieun Oh, Chenghao Zhu, Nicole Zeltser, Constance H. Li, Brandon L. Tsai, Paul C. Boutros
Journal: Cancer Research (2023)

Abstract Sex differences have been observed in the incidence, prognosis and mortality of many different adult cancer types, linked to differences in tumor genomics. By contrast, sex differences in pediatric cancers have been understudied, with almost no genomic studies. To fill this gap, we have performed analyses on the genome, epigenome and transcriptome in eight different pediatric cancer types in nearly 3,000 tumors. Pediatric cancers had distinctive somatic mutational patterns when it came to sex differences, with acute lymphoblastic leukemia exhibiting sex-biases in its transcriptome and other cancer types showing stronger biases in their methylomes. However, no sex differences in somatic mutational profiles were identified. This stands in stark contrast to adult tumors, where we further previous genomic and transcriptomic studies by identifying sex differences in the proteomes, in drug sensitivity profiles and in functional genomics. In summary, our study reveals that sex differences in pediatric cancers are more modest than those in adult tumors and this may shed light into potential mechanisms by which sex influences the cancer genome. Citation Format: Jieun Oh, Chenghao Zhu, Nicole Zeltser, Constance H. Li, Brandon L. Tsai, Paul C. Boutros. Sex differences in pediatric cancer genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3120.
Abstract 691: Irradiated whole tumor cells pulsed with mannan-BAM, TLR ligands and anti-CD40 antibody serve as a potent tumor cell vaccine against glioblastoma
Authors: Herui Wang, Rogelio Medina, Juan Ye, Samik Chakraborty, Ondrej Uher, Mitchell Sun, Jan Zenka, Mark R. Gilbert, Karel Pacak, Zhengping Zhuang
Journal: Cancer Research (2023)

Abstract Despite numerous therapeutic advances in cancers, the treatment of glioblastoma multiforme (GBM) remains a challenge. Boosting T-lymphocyte mediated responses against GBM offers a promising approach towards solving this problem. Herein, we present a therapeutic vaccination strategy that promotes the phagocytosis of tumor cells, enhances tumor antigen presentation, and induces a tumor-specific adaptive immune response with subsequent tumor eradication. This strategy consists of subcutaneous injection of irradiated whole tumor cells (rWTC) pulsed with phagocytic agonists (Mannan-BAM), TLR ligands (LTA, Poly (I:C), and R-848), and anti-CD40 agonistic antibody (collectively abbreviated as rWTC-MBTA). We evaluated the therapeutic efficacy of rWTC-MBTA strategy in mouse syngeneic GBM tumor models with GL261 and SB28 cells. In GL261 GBM model, complete regression (CR) of intracranial tumors was achieved in 70% (7/10) of rWTC-MBTA treated animals while none survived in the control group. Of note, the therapeutic efficacy of rWTC-MBTA was abolished in CD4-T and/or CD8-T lymphocyte depleted mice. Immunophenotyping analyses of peripheral lymph nodes and brain tumors of rWTC-MBTA treated mice demonstrated increased antigen presenting cells (dendritic cells and MHC II+ monocytes) and increased cytotoxic IFNγ, TNFα, and granzyme B-secreting CD4-T and CD8-T cells. All three CR mice that were rechallenged with GL261 cells intracranially 14 months after their last rWTC-MBTA treatment resisted tumor development, confirming the establishment of long-term immunological memory. In SB28 GBM model, 80% (8/10) rWTC-MBTA treated mice survived past 95 days after tumor cell implantation without any GBM-related symptoms, with median survival being only 35 days in control groups. In summary, our study demonstrated that rWTC-MBTA strategy can induce potent adaptive immune response against GBM in pre-clinical models. Citation Format: Herui Wang, Rogelio Medina, Juan Ye, Samik Chakraborty, Ondrej Uher, Mitchell Sun, Jan Zenka, Mark R. Gilbert, Karel Pacak, Zhengping Zhuang. Irradiated whole tumor cells pulsed with mannan-BAM, TLR ligands and anti-CD40 antibody serve as a potent tumor cell vaccine against glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 691.
Abstract 5165: In vivo therapeutic validation of NRT-YHD_001, a novel macrophage checkpoint inhibitor, in liver cancer
Authors: Suk Woo Nam, Sangyean Kim, Min Jeong Na, Eunbi Shin, Jin Woong Ha, Soyoung Jeon, Jeong Hwan Yoon
Journal: Cancer Research (2023)

Abstract Previously, we demonstrated that recovery of Histone deacetylase 6 (HDAC6) elicited let-7i-5p suppression to de-repress the thrombospondin-1 (TSP1) expression, and thereby it occupied CD47 receptor to block CD47-SIRPα mediated anti-phagocytosis of macrophage in liver cancer. NRT-YHD_001 is a modified antisense miRNA of let-7i-5p for liver cancer treatment. NRT-YHD_001 was substituted with O-methoxyethyl and phosphothioate for stability, and N-acetylgalactosamine was attached for specific delivery to the liver. In in vitro phagocytosis assay, NRT-YHD_001 showed macrophage phagocytosis activity with similar or better results compared to non-modified antisense let-7i-5p (AS_let-7i-5p). In addition, it was confirmed that NRT-YHD_001 inhibited endogenous let-7i-5p of liver cancer cells and activated macrophage phagocytosis at 4°C or 25°C for up to 2 weeks. When NRT-YHD_001 activity was investigated in vivo after 1 week, 2 weeks, and 4 weeks after administration of single dose NRT-YHD_001 to the tail vein of a mouse, NRT-YHD_001 was not degraded, and let-7i-5p was inhibited while maintaining activity in liver tissue for 2 weeks after injection. To investigate the in vivo therapeutic effect, a mouse spontaneous (Ras-transgenic) liver cancer model was used and compared with the sorafenib-administered group. After administration of NRT-YHD_001 and sorafenib each week at the time when liver mass was detected, the tumor size and growth rate were compared. As a result, the NRT-YHD_001 administration group showed significant therapeutic effect compared to sorafenib. These results showed that NRT-YHD_001 had a strong anticancer effect by converting the macrophage of don't eat me into eat me signal in the tumor microenvironment of liver cancer, thereby removing or inhibiting liver cancer cells. Keywords: let-7i-5p, macrophage, phagocytosis, liver cancer, NRT-YHD_001 Citation Format: Suk Woo Nam, Sangyean Kim, Min Jeong Na, Eunbi Shin, Jin Woong Ha, Soyoung Jeon, Jeong Hwan Yoon. In vivo therapeutic validation of NRT-YHD_001, a novel macrophage checkpoint inhibitor, in liver cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5165.
Abstract 1736: Role of brain fatty acid binding protein in glioblastoma microtube formation
Authors: Won-Shik Choi, Caitlin Mak, John M. Githaka, Darryl Glubrecht, Pureunsol Jeon, Roseline Godbout
Journal: Cancer Research (2023)

Abstract Glioblastoma (GBM) is a highly infiltrative brain cancer with a dismal prognosis. Conventional treatment using surgery, radiation therapy, and chemotherapy (usually temozolomide) invariably fails. GBM microtubes, which are ultra-long membrane-enclosed protrusions, are associated with therapy resistance and are believed to function by forming multicellular communication networks. Growth-associated protein GAP43 is an important protein for GBM microtube formation. Although lipids are important for GBM progression, the roles of lipid chaperones such as the fatty acid-binding proteins (FABPs) are not well understood. FABPs are involved in fatty acid uptake from the microenvironment and intracellular transport of fatty acids. Brain fatty acid binding protein (FABP7) is highly expressed and is associated with a poor prognosis in GBM. FABP7 levels increase in therapy-resistant GBM cells, suggesting that FABP7 provides a cancer cell survival advantage when GBMs are treated with conventional therapy. FABP7 has a high affinity for polyunsaturated fatty acids (PUFAs), such as omega-3 docosahexaenoic acid (DHA) and omega-6 arachidonic acid (AA), both of which are abundant in brain. Previous studies have shown a correlation between FABP7 expression, increased neural stem cell properties, and increased cell migration in glioblastoma cells, especially when FABP7 is bound to AA. We have recently found that FABP7 is expressed in microtubes, leading to the hypothesis that FABP7 along with its fatty acid ligands can be transported to sites distant from the main tumor mass through these connecting tubes. We are studying the mechanism of action of FABP7 in microtubes by: (i) examining the effect of DHA and AA, as well as FABP7 inhibition on microtube formation and cell migration, and (ii) using both neurosphere cultures and animal models of glioblastoma to investigate the pathways that are activated by FABP7. Our results to date support the use of FABP7 inhibitors to sensitize therapy-resistant cells as part of the standard-of-care for the treatment of GBM patients. Citation Format: Won-Shik Choi, Caitlin Mak, John M. Githaka, Darryl Glubrecht, Pureunsol Jeon, Roseline Godbout. Role of brain fatty acid binding protein in glioblastoma microtube formation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1736.
Abstract 4386: Comparison of cytotoxicity of anthracycline based antineoplastic drugs in breast cancer
Authors: Mitali Singhal, Jacobo Elies Gomez, Sanjit Nayak, Kirsten Riches Suman, Amalia Ruiz Estrada
Journal: Cancer Research (2023)

Abstract Mitoxantrone (MTX) is used for the chemotherapeutic treatment of breast cancer, but it has a dose-limiting cardiotoxicity. One of the mechanisms of MTX cytotoxicity is by inhibiting the topoisomerase II enzyme, which is crucial for maintaining cellular processes like replication. The aim of the study is to investigate if an alternative analog of MTX, named KP71 would be a suitable antineoplastic drug with reduced cardiovascular side effects. Cytotoxicity of both drugs in breast cancer cell lines MDA-MB-468, MDA-MB-231, MCF7, the non-neoplastic breast cell line MCF10, cardiac human fibroblasts (HFB), and human umbilical vein endothelial cells (HUVEC) was assessed by MTT at 96h. The IC50 values (nM) for MTX/KP71 were as shown in table below. DNA decatenation assay demonstrated topoisomerase II inhibition with values of IC50 = 2.9/12.3 µM for topoisomerase IIα, and 2.1/7.0 µM for topoisomerase IIβ for MTX/KP71 respectively. Western blotting showed DNA damage by the gradation in γH2AX expression at different concentrations of MTX and KP71 at 6 h and 24 h treatment. KP71 was found to retain the ability to inhibit the proliferation of neoplastic cell lines in vitro with a slower profile of cytotoxicity on non-neoplastic cell lines as compared to MTX. KP71 partly exerted cytotoxicity by damaging DNA and inhibiting topoisomerase II enzyme activity. Organotypic HFB-HUVEC co-cultures were used to investigate the effects of anthracycline drugs in angiogenesis. Although both drugs reduced the number of tubules (and branches) compared to control (absence of drug), there were not significant differences between MTX and KP71. MTT IC50 (nM) MTX KP71 MDA-MB-468 27 50 MDA-MB231 38 169 MCF7 63 150 MCF10 35 90 HFB 160 1177 HUVEC 56 93 Citation Format: Mitali Singhal, Jacobo Elies Gomez, Sanjit Nayak, Kirsten Riches Suman, Amalia Ruiz Estrada. Comparison of cytotoxicity of anthracycline based antineoplastic drugs in breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4386.